Coelacanth assembly and gene annotation

Assembly

This is the preliminary display of the Coelacanth (Latimeria chalumnae) genome produced by the
Broad Institute.
Illumina techology was used to produced this high quality draft. The whole genome shotgun data was assembled with Allpaths.
The genome is 2.9gb in length;,composed of 291,828 contigs with an N50 value of 12.6kb and 22,818 scaffolds with an N50 value of 765kb.

Gene annotation

The Ensembl genome annotation pipeline was used to identify genes. Models built from Coelacanth proteins and cDNAs have been given priority over predictions from other vertebrate species. 6,671 transcript models made from paired end Illumina RNA-Seq were added into the gene set where they added a novel model or splice variant. RNA-Seq data was also used to add UTR to non species specific models. The total gene set contains 19,697 protein coding genes with a further 2,894 ncRNAs and 141 pseudogenes.

More information

Statistics

Summary

<p>
The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).
</p>Golden Path Length

2,860,591,921

Annotation method

Full genebuild

Genebuild started

Sep 2011

Genebuild released

Oct 2011

Genebuild last updated/patched

Nov 2012

Database version

92.1

Gene counts

<p>A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.</p>Pseudogenes

141

Nucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.Gene transcripts